Inviscid three-dimensional free surface wave motions are simulated using a novel quadratic higher order boundary element model (HOBEM) based on potential theory for irrotational, incompressible fluid flow in an infinite water-depth. The free surface boundary conditions are fully non-linear. Based on the use of images, a channel Green function is developed and applied to the present model so that two lateral surfaces of an infinite-depth wave tank can be excluded from the calculation domain. In order to generate incident waves and dissipate outgoing waves, a non-reflective wave generator, composed of a series of vertically aligned point sources in the computational domain, is used in conjunction with upstream and downstream damping layers. Numerical experiments are carried out, with linear and fully non-linear, regular and focused waves. It can be seen from the results that the present approach is effective in generating a specified wave profile in an infinite water-depth without reflection at the open boundaries, and fully non-linear numerical simulations compare well with theoretical solutions. The present numerical technique is aimed at efficient modelling of the non-linear wave interactions with ocean structures in deep water.